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Sample GSM706685 Query DataSets for GSM706685
Status Public on Apr 21, 2011
Title Control_CpG_Methylation_bisulfite_sequencing
Sample type SRA
 
Source name J1 ES cells, control siRNA
Organism Mus musculus
Characteristics cell line: J1
cell type: mouse embryonic stem (MES) cells
sirna treatment: control siRNA
Treatment protocol J1 ES cells were transfected with control siRNA or Tet1 siRNA and harvested four days after transfection. The genomic DNA was purified, and bisulfite conversion was performed with the EZ-Methylation Gold kit (Zymo Research).
Growth protocol J1 ES cells were co-cultured with MEF feeder cells in standard ES cell medium.
Extracted molecule genomic DNA
Extraction protocol A library of 55,000 long oligonucleotides was designed to capture the transcription start sites of 908 genes on mouse chromosomes X and Y, 114 imprinted genes, 493 miRNA genes and 88 additional targets. The oligonucleotide library was PCR-amplified and converted into functional padlock probes through a series of enzymatic reactions as described previously (Zhang et al., 2009). The genomic DNA was purified using the DNeasy kit (Qiagen), and bisulfite conversion was performed with the EZ-Methylation Gold kit (Zymo Research). Target capture was performed on 200ng of bisulfite-converted DNA with 100x excess of padlock probes. The detailed protocol is described in the reference: Deng, J. et al. Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotech, 2009, 27, 353-360 (PMID 19330000).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer IIx
 
Description CpG DNA methylation.

library strategy: USER-S1-Ligation
library selection: padlock capture
Data processing Reads were aligned to captured target sequences. CpG methylation levels were extracted from mapped reads. The resulting values are real numbers ranging from 0 to 1, which correspond to completely unmethylated and completely methylated, respectively.
 
Submission date Apr 11, 2011
Last update date May 15, 2019
Contact name Feizhen Wu
E-mail(s) wufz@fudan.edu.cn
Phone 86-21-54237821
Organization name Fudan Univ, Shanghai, China
Department Institutes of Biomedical Sciences
Lab Epigenetics lab
Street address Dongan Road 131, Rm 511 Mingdao Building
City Shanghai
State/province Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL11002
Series (2)
GSE28500 Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells
GSE28533 Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells (bisulfite sequencing data)
Relations
SRA SRX057753
BioSample SAMN02198511
Named Annotation GSM706685_Control_CpG_Methylation_bisulfite_sequencing.BED.gz

Supplementary file Size Download File type/resource
GSM706685_Control_CpG_Methylation_bisulfite_sequencing.BED.gz 259.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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